<i>Parmelia sulcata</i>(Ascomycota:<i>Parmeliaceae</i>), a sympatric monophyletic species complex

Molina, Marı́a del Carmen; Divakar, Pradeep K.; Millanes, Ana M.; Sánchez, Edinson; Del-Prado, Ruth; Hawksworth, David L.; Crespo, Ana

doi:10.1017/s0024282911000521

Cited by 49 publications

(60 citation statements)

References 93 publications

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“…In spite of the limitations in delimiting taxa using molecular data, the effective use of genetic data appears to be essential to appropriately and practically identify natural groups in some phenotypically cryptic lichen-forming fungal lineages (Divakar et al 2010b;Leavitt et al 2011b;Leavitt et al 2011c;Molina et al 2011b;Pino-Bodas et al 2011;Pino-Bodas et al 2012), including R. melanophthalma s.l. This does not preclude the fact that additional studies investigating morphological and chemical characters may potentially identify independent characters, or combinations of characters, supporting species circumscribed using molecular data.…”

Section: Discussionmentioning

confidence: 99%

DNA barcode identification of lichen-forming fungal species in the Rhizoplaca melanophthalma species-complex (Lecanorales, Lecanoraceae), including five new species

Leavitt¹,

Fernández-Mendoza²,

Pérez‐Ortega³

et al. 2013

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Citation: Leavitt SD, Fernández-Mendoza F, Pérez-Ortega S, Sohrabi M, Divakar PK, Lumbsch TH, St. Clair LLS (2013) DNA barcode identification of lichen-forming fungal species in the Rhizoplaca melanophthalma species-complex (Lecanorales, Lecanoraceae), including five new species. MycoKeys 7: 1-22. doi: 10.3897/mycokeys.7.4508 Abstract Recent studies using sequence data from multiple loci and coalescent-based species delimitation have revealed several species-level lineages within the phenotypically circumscribed taxon Rhizoplaca melanophthalma sensu lato. Here, we formally describe five new species within this group, R. occulta, R. parilis, R. polymorpha, R. porterii, and R. shushanii, using support from the coalescent-based species delimitation method implemented in the program Bayesian Phylogenetics and Phylogeography (BPP) as the diagnostic feature distinguishing new species. We provide a reference DNA sequence database using the ITS marker as a DNA barcode for identifying species within this complex. We also assessed intraspecific genetic distances within the six R. melanophthalma sensu lato species. While intraspecific genetic distances within the five new species were less than or equal to the lowest interspecific pairwise comparison values, an overlap in genetic distances within the R. melanophthalma sensu stricto clade suggests the potential for additional Leavitt et al. / MycoKeys 7: 1-22 (2013) 2 phenotypically cryptic lineages within this broadly distributed lineage. Overall, our results demonstrate the potential for accurately identifying species within the R. melanophthalma group by using molecularbased identification methods.

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Section: Discussionmentioning

confidence: 99%

DNA barcode identification of lichen-forming fungal species in the Rhizoplaca melanophthalma species-complex (Lecanorales, Lecanoraceae), including five new species

Leavitt¹,

Fernández-Mendoza²,

Pérez‐Ortega³

et al. 2013

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“…Our data from the H . hypotrypa group suggest a more complex relationship between esorediate and sorediate populations, including the presence of reproductively uniform species being closely related to lineages exhibiting different reproductive modes [90] or the presence of several sorediate populations each representing distinct lineages [91,92]. Despite the fact that in the majority of cases studied using molecular data sorediate and esorediate populations were found to represent variations within one species, no conclusions can be drawn a priori .…”

Section: Discussionmentioning

confidence: 99%

Limitations of Species Delimitation Based on Phylogenetic Analyses: A Case Study in the Hypogymnia hypotrypa Group (Parmeliaceae, Ascomycota)

et al. 2016

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Delimiting species boundaries among closely related lineages often requires a range of independent data sets and analytical approaches. Similar to other organismal groups, robust species circumscriptions in fungi are increasingly investigated within an empirical framework. Here we attempt to delimit species boundaries in a closely related clade of lichen-forming fungi endemic to Asia, the Hypogymnia hypotrypa group (Parmeliaceae). In the current classification, the Hypogymnia hypotrypa group includes two species: H. hypotrypa and H. flavida, which are separated based on distinctive reproductive modes, the former producing soredia but absent in the latter. We reexamined the relationship between these two species using phenotypic characters and molecular sequence data (ITS, GPD, and MCM7 sequences) to address species boundaries in this group. In addition to morphological investigations, we used Bayesian clustering to identify potential genetic groups in the H. hypotrypa/H. flavida clade. We also used a variety of empirical, sequence-based species delimitation approaches, including: the “Automatic Barcode Gap Discovery” (ABGD), the Poisson tree process model (PTP), the General Mixed Yule Coalescent (GMYC), and the multispecies coalescent approach BPP. Different species delimitation scenarios were compared using Bayes factors delimitation analysis, in addition to comparisons of pairwise genetic distances, pairwise fixation indices (FST). The majority of the species delimitation analyses implemented in this study failed to support H. hypotrypa and H. flavida as distinct lineages, as did the Bayesian clustering analysis. However, strong support for the evolutionary independence of H. hypotrypa and H. flavida was inferred using BPP and further supported by Bayes factor delimitation. In spite of rigorous morphological comparisons and a wide range of sequence-based approaches to delimit species, species boundaries in the H. hypotrypa group remain uncertain. This study reveals the potential limitations of relying on distinct reproductive strategies as diagnostic taxonomic characters for Hypogymnia and also the challenges of using popular sequence-based species delimitation methods in groups with recent diversification histories.

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“…Diverse examples of widely distributed nominal taxa masking multiple, species-level diversity include: Cladia aggregata (Parnmen et al 2012), Melanelixia glabra (Divakar et al 2010a), Melanelixia fuliginosa/M. glabratula , Melanohalea elegantula, M. exasperata (Leavitt et al 2013a), Montanelia tominii (Leavitt et al 2015b), Parmelia saxatilis (Molina et al 2011a), P. sulcata , Molina et al 2011b, Parmelina quercina (Argüello et al 2007), P. tiliacea (Nuñez-Zapata et al 2011), Protoparmelia badia , Physconia distorta , Rhizoplaca melanophthalma (Leavitt et al 2013b), and Sphaerophorus globosus (Högnabba and Wedin 2003). These studies demonstrate that some supposedly cosmopolitan taxa may include previously unrecognized diversity.…”

Section: Introductionmentioning

confidence: 99%

Phylogenetic studies uncover a predominantly African lineage in a widely distributed lichen-forming fungal species

Kirika¹,

Divakar²,

Crespo³

et al. 2016

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Citation: Kirika PM, Divakar PK, Crespo A, Mugambi G, Orock EA, Leavitt SD, Gatheri GW, Lumbsch HT (2016) Phylogenetic studies uncover a predominantly African lineage in a widely distributed lichen-forming fungal species. MycoKeys 14: 1-16. doi: 10.3897/mycokeys.14.8971 Abstract A number of lichen-forming fungal species are widely distributed. Here, we investigate biogeographic patterns in a widely distributed isidiate taxon -Parmelinella wallichiana -using molecular sequence data. Our results revealed that Parmelinella wallichina, as currently circumscribed, is not monophyletic but falls into four clades, two of them represented by a sample only. A third clade, occurring in Africa and southern India is described as a new species, Parmelinella schimperiana Kirika & Divakar, sp. nov. Our study adds a further example of previously overlooked, geographically distinct, lineages that were discovered using molecular data.

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Parmelia sulcata(Ascomycota:Parmeliaceae), a sympatric monophyletic species complex

Cited by 49 publications

References 93 publications

DNA barcode identification of lichen-forming fungal species in the Rhizoplaca melanophthalma species-complex (Lecanorales, Lecanoraceae), including five new species

DNA barcode identification of lichen-forming fungal species in the Rhizoplaca melanophthalma species-complex (Lecanorales, Lecanoraceae), including five new species

Limitations of Species Delimitation Based on Phylogenetic Analyses: A Case Study in the Hypogymnia hypotrypa Group (Parmeliaceae, Ascomycota)

Phylogenetic studies uncover a predominantly African lineage in a widely distributed lichen-forming fungal species

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